Elaine,
A rootkit is a type of virus that embeds itself deeply within the computer and is usually impossible for normal antivirus apps to find and remove, once in. They often work by generating new mini-programs from time to time that actually do the tasks the malware wishes to achieve (usually obtaining data and phoning home with it, or sending you to websites that perform additional tasks). The mini-apps can be found but the main app itself is camouflaged too well.
The best protection is a top-quality antivirus like Avast or AVG, plus a firewall that actually works such as Online Armor, which generally stop these attacks before they are successful. Once in, they are very hard to get rid of. Some people make sure their machines are clean by making a disk image of a clean Windows install plus the normal apps needed (with Acronis, Macrium etc), before it has been connected to the web or had any other media connected, so it's as clean as can be obtained.
Then, they wipe their PC every 6 months and reinstall the image. It takes about 15 minutes to get up and running again instead of the 4 hours it would take to reinstall Windows and the normal working apps. To find out more on this, google 'drive imaging' or just go to Gizmo's Freeware for advice on it (the ECF of free software).
